[Debichem-commits] r1341 - in /unstable/pymol/debian: changelog control patches/11_fix__cmd_import.dpatch pymol.1 rules

dleidert-guest at users.alioth.debian.org dleidert-guest at users.alioth.debian.org
Mon May 5 23:59:45 UTC 2008


Author: dleidert-guest
Date: Mon May  5 23:59:45 2008
New Revision: 1341

URL: http://svn.debian.org/wsvn/debichem/?sc=1&rev=1341
Log:
* debian/control (Uploaders): Added myself.
* debian/pymol.1: Added basic man-page for pymol (closes: #148399).
* debian/rules (binary-arch): Install man-page for pymol.
* debian/patches/11_fix__cmd_import.dpatch: Added a short description based
  on the changelog entry to satisfy lintian.

Added:
    unstable/pymol/debian/pymol.1
Modified:
    unstable/pymol/debian/changelog
    unstable/pymol/debian/control
    unstable/pymol/debian/patches/11_fix__cmd_import.dpatch
    unstable/pymol/debian/rules

Modified: unstable/pymol/debian/changelog
URL: http://svn.debian.org/wsvn/debichem/unstable/pymol/debian/changelog?rev=1341&op=diff
==============================================================================
--- unstable/pymol/debian/changelog (original)
+++ unstable/pymol/debian/changelog Mon May  5 23:59:45 2008
@@ -1,3 +1,13 @@
+pymol (1.1~beta3-4) UNRELEASED; urgency=low
+
+  * debian/control (Uploaders): Added myself.
+  * debian/pymol.1: Added basic man-page for pymol (closes: #148399).
+  * debian/rules (binary-arch): Install man-page for pymol.
+  * debian/patches/11_fix__cmd_import.dpatch: Added a short description based
+    on the changelog entry to satisfy lintian.
+
+ -- Daniel Leidert (dale) <daniel.leidert at wgdd.de>  Tue, 06 May 2008 01:50:29 +0200
+
 pymol (1.1~beta3-3) unstable; urgency=low
 
   [ LI Daobing ]

Modified: unstable/pymol/debian/control
URL: http://svn.debian.org/wsvn/debichem/unstable/pymol/debian/control?rev=1341&op=diff
==============================================================================
--- unstable/pymol/debian/control (original)
+++ unstable/pymol/debian/control Mon May  5 23:59:45 2008
@@ -3,7 +3,8 @@
 Priority: optional
 Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
 Uploaders: Michael Banck <mbanck at debian.org>,
- LI Daobing <lidaobing at gmail.com>
+ LI Daobing <lidaobing at gmail.com>,
+ Daniel Leidert (dale) <daniel.leidert at wgdd.de>
 Build-Depends: debhelper (>= 5), dpatch, python-dev, python-numeric, glutg3-dev, libpng12-0-dev, tk8.4-dev, libfreetype6-dev, python-support (>= 0.4), g++-4.2 [arm armel]
 Standards-Version: 3.7.3
 Homepage: http://pymol.sourceforge.net

Modified: unstable/pymol/debian/patches/11_fix__cmd_import.dpatch
URL: http://svn.debian.org/wsvn/debichem/unstable/pymol/debian/patches/11_fix__cmd_import.dpatch?rev=1341&op=diff
==============================================================================
--- unstable/pymol/debian/patches/11_fix__cmd_import.dpatch (original)
+++ unstable/pymol/debian/patches/11_fix__cmd_import.dpatch Mon May  5 23:59:45 2008
@@ -2,7 +2,7 @@
 ## 11_fix__cmd_import.dpatch by Pierre Habouzit <madcoder at debian.org>
 ##
 ## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
+## DP: Fixes an import that does not behave well.
 
 @DPATCH@
 diff -urNad pymol-0.98+0.99rc6~/modules/pymol/__init__.py pymol-0.98+0.99rc6/modules/pymol/__init__.py

Added: unstable/pymol/debian/pymol.1
URL: http://svn.debian.org/wsvn/debichem/unstable/pymol/debian/pymol.1?rev=1341&op=file
==============================================================================
--- unstable/pymol/debian/pymol.1 (added)
+++ unstable/pymol/debian/pymol.1 Mon May  5 23:59:45 2008
@@ -1,0 +1,128 @@
+.TH "PYMOL" "1" "2008-05-06" "" "User commands"
+
+.SH NAME
+pymol \- free and flexible molecular graphics and modelling package
+
+.SH SYNOPSIS
+.B pymol
+.RB [ options ]
+.RI [ files ]
+
+.SH DESCRIPTION
+Over the years, PyMOL has become a capable molecular viewer with support for
+animations, high-quality rendering, crystallography, and other common molecular
+graphics activities. It has been adopted by many hundreds (perhaps even
+thousands) of scientists spread over thirty countries. However, PyMOL is still
+very much a work in progress, with development expected to continue for years
+to come.
+
+.SH OPTIONS
+These options are currently supported:
+
+.TP
+.B \-2   
+Start in two-button mouse mode.
+.TP
+.B \-c
+Command line mode, no GUI.  For batch opeations.
+.TP
+.BI \-d " string"
+Run pymol command string upon startup.
+.TP
+.B \-e   
+Start in full-screen mode.
+.TP
+.BI \-f " #line"
+Controls display of commands and feedback in OpenGL (\fB0\fR=\fIoff\fR).
+.TP
+.BI \-g " file.png"
+Write a PNG file (after evaluating previous arguments)
+.TP
+.B \-i
+Disable the internal OpenGL GUI (object list, menus, etc.)
+.TP
+.BI \-l " file.py"
+Spawn a python program in new thread.
+.TP
+.B \-o   
+Disable security protections for session files.
+.TP
+.B \-p   
+Listen for commands on standard input.
+.TP
+.B \-q
+Quiet launch. Suppress splash screen & other chatter.
+.TP
+.BI \-r " file.py"
+Run a Python program (in \fI__main__\fR) on startup.
+.TP
+.BI \-s " script"
+Save commands to this PyMOL script or program file.
+.TP
+.B \-t
+Use Tcl/Tk based external GUI module (\fIpmg_tk\fR).
+.TP
+.BI \-u " script"
+Load and append to this PyMOL script or program file.
+.TP
+.B \-x   
+Disable the external GUI module.
+.TP
+.B \-B
+Enable blue-line stereo signal (for Mac stereo)
+.TP
+.B \-G
+Start in Game mode.
+.TP
+.B \-M
+Force mono even when hardware stereo is present.
+.TP
+.B \-R
+Launch Greg Landrum's XMLRPC listener.
+.TP
+.B \-S
+Force and launch in stereo, if possible.
+.TP
+.BI \-X " int " \-Y " int " \-W " int " \-H " int " \-V " int "
+Adjust window geometry.
+
+.PP
+All \fIfiles\fR provided will be loaded or run after PyMOL starts. 
+They can have one of the following extensions:
+.sp
+.nf
+\&\.pml            PyMOL command script to be run on startup
+\&\.py[cm]         Python program to be run on startup
+\&\.pdb            Protein Data Bank format file to be loaded on startup
+\&\.mmod           Macromodel format to be loaded on startup
+\&\.mol            MDL MOL file to be loaded on startup
+\&\.sdf            MDL SD file to be parsed and loaded on startup
+\&\.xplor          X-PLOR Map file (ASCII) to be loaded on startup
+\&\.ccp4           CCP4 map file (BINARY) to be loaded on startup
+\&\.cc[12]         ChemDraw 3D cartesian coordinate file
+\&\.pkl            Pickled ChemPy Model (class "\fIchempy.model.Indexed\fR")
+\&\.r3d            Raster3D file
+\&\.cex            CEX file (Metaphorics)
+\&\.top            AMBER topology file
+\&\.crd            AMBER coordinate file
+\&\.rst            AMBER restart file
+\&\.trj            AMBER trajectory
+\&\.pse            PyMOL session file
+\&\.phi            Delphi/Grasp Electrostatic Potential Map 
+.fi
+
+.PP
+For a list of options, you can also enter the following in the command line
+of \fBpymol\fR:
+.IP
+.B help launching
+
+.SH COMMANDS
+Please refer to PyMols online documentation
+at \fI\%http://www.pymolwiki.org/index.php/Category:Commands\%\fR or its internal
+help for a command reference.
+
+.SH AUTHOR
+This manpage was written by \fBDaniel Leidert\fR <\&daniel.leidert at wgdd.de\&>
+for the Debian distribution (but may be used by others).
+

Modified: unstable/pymol/debian/rules
URL: http://svn.debian.org/wsvn/debichem/unstable/pymol/debian/rules?rev=1341&op=diff
==============================================================================
--- unstable/pymol/debian/rules (original)
+++ unstable/pymol/debian/rules Mon May  5 23:59:45 2008
@@ -89,7 +89,7 @@
 	chmod -x $(BUILD_DIR)/usr/share/pymol/cmyk.png
 	dh_installdocs -A AUTHORS DEVELOPERS README
 	dh_installchangelogs ChangeLog
-#	dh_undocumented pymol.1
+	dh_installman debian/pymol.1
 	dh_link
 	dh_pysupport
 	dh_strip 




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